From a0b64dd539ff544ba925f4b3b1445e25965876f3 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 31 Mar 2011 11:05:48 +0000
Subject: [PATCH] add options to command line
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15859 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 59 +++++++++++++++++--
1 file changed, 55 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 0f59c9679..46557a457 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -3159,7 +3159,13 @@ public class BamView extends JPanel
bam.add(args[i]);
}
int nbasesInView = 1000;
-
+ String chr = null;
+ String vw = null;
+ boolean orientation = false;
+ boolean covPlot = false;
+ boolean snpPlot = false;
+ int base = 0;
+
for(int i=0;i<args.length; i++)
{
if(args[i].equals("-a"))
@@ -3176,18 +3182,35 @@ public class BamView extends JPanel
}
else if(args[i].equals("-r"))
reference = args[++i];
- else if(args[i].equals("-v"))
+ else if(args[i].equals("-n"))
nbasesInView = Integer.parseInt(args[++i]);
else if(args[i].equals("-s"))
System.setProperty("samtoolDir", args[++i]);
+ else if(args[i].equals("-c"))
+ chr = args[++i].trim();
+ else if(args[i].equals("-b"))
+ base = Integer.parseInt(args[++i].trim());
+ else if(args[i].equals("-v"))
+ vw = args[++i].trim();
+ else if(args[i].equals("-o"))
+ orientation = true;
+ else if(args[i].equals("-pc"))
+ covPlot = true;
+ else if(args[i].equals("-ps"))
+ snpPlot = true;
else if(args[i].startsWith("-h"))
{
System.out.println("-h\t show help");
System.out.println("-a\t BAM/SAM file to display");
System.out.println("-r\t reference file (optional)");
- System.out.println("-v\t number of bases to display in the view (optional)");
- /*System.out.println("-s\t samtool directory");*/
+ System.out.println("-n\t number of bases to display in the view (optional)");
+ System.out.println("-c\t chromosome name (optional)");
+ System.out.println("-v\t view (optional - IS (inferred size), S (stack, default), PS (paired stack), ST (strand), C (coverage))");
+ System.out.println("-b\t base position (optional)");
+ System.out.println("-o\t show orientation (optional)");
+ System.out.println("-pc\t plot coverage (optional)");
+ System.out.println("-ps\t plot SNP (optional and only with -r)");
System.exit(0);
}
}
@@ -3196,6 +3219,34 @@ public class BamView extends JPanel
(JPanel)frame.getContentPane(), frame);
frame.setTitle("BamView v"+view.getVersion());
+ if(chr != null)
+ view.combo.setSelectedItem(chr);
+ if(vw != null)
+ {
+ if(vw.equalsIgnoreCase("IS"))
+ view.cbIsizeStackView.setSelected(true);
+ if(vw.equalsIgnoreCase("PS"))
+ view.cbPairedStackView.setSelected(true);
+ if(vw.equalsIgnoreCase("ST"))
+ view.cbStrandStackView.setSelected(true);
+ if(vw.equalsIgnoreCase("C"))
+ view.cbCoverageView.setSelected(true);
+ }
+ if(base > 0)
+ view.scrollBar.setValue(base);
+ if(orientation)
+ view.isOrientation = true;
+ if(covPlot)
+ {
+ view.isCoverage = true;
+ view.coveragePanel.setVisible(true);
+ }
+ if(snpPlot)
+ {
+ view.isSNPplot = true;
+ view.snpPanel.setVisible(true);
+ }
+
// translucent
//frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f));
frame.addWindowFocusListener(new WindowFocusListener()
--
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